We carried out DNA microarray-based global expression profiling of all preimplantation stages in mouse. They revealed and characterized the distinctive patterns of maternal RNA degradation and two major transient waves of de novo transcription: zygotic genome activation (ZGA) and mid-preimplantation gene activation (MGA). Through these analyses, we identified a number of genes that show unique expression patterns. We have demonstrated that one of them, named Zscan4, is expressed exclusively in 2-cell mouse embryos and ES cells and plays a critical role in the progression of preimplantation development. We also identified a gene, named Trim43, whose expression began at the 2-cell stage, peaked at the 8-cell/morula stage, and dramatically fell by the blastocyst stage. Another gene (Chuk) shows constant RNA levels throughout preimplantation development and can be used as an internal standard suitable for quantitative RT-PCR. We also developed a technique to do large-scale Whole Mount In Situ Hybridization (WISH), which allows us to reveal the spatial expression patterns of 91 genes in mouse preimplantation embryos. We are currently studying the functions of these genes in detail.